If you go a higher end Capsule Hotel, such as First Cabin then they have very nice shower cubicles and communal bath in a common washroom area.
You can stay at the capsule hotel for only 2,000 yenï½ž/per night!. You would sleep inside this capsule room, and use common bathroom and shower room.
Thank you for your inquiry. Yes, we do have showers but as it's stated in the above response, we have Japanese style shower area where each section is .
Shinjuku Kuyakushomae Capsule Hotel, Shinjuku Picture: The shower room – Check out TripAdvisor members' 23736 candid photos and videos of Shinjuku .